Tag-Free Internal RNA Labeling and Photocaging Based on mRNA Methyltransferases

The mRNA modification N-6-methyladenosine (m(6)A) is associated with multiple roles in cell function and disease. The methyltransferases METTL3-METTL14 and METTL16 act as writers for different target transcripts and sequence motifs. The modification is perceived by dedicated reader and eraser proteins, but not by polymerases. We report that METTL3-14 shows remarkable cosubstrate promiscuity, enabling sequence-specific internal labeling of RNA without additional guide RNAs. The transfer of ortho-nitrobenzyl and 6-nitropiperonyl groups allowed enzymatic photocaging of RNA in the consensus motif, which impaired polymerase-catalyzed primer extension in a reversible manner. METTL16 was less promiscuous but suitable for chemo-enzymatic labeling using different types of click chemistry. Since both enzymes act on distinct sequence motifs, their combination allowed orthogonal chemo-enzymatic modification of different sites in a single RNA.

Automated summary

mRNA modification N-6-methyladenosine plays important roles in cell function and disease. The methyltransferases METTL3-METTL14 and METTL16 can specifically label RNA at different sites, enabling orthogonal chemo-enzymatic modification.